Merge pull request #268 from CanDIG/mshadbolt/percent-pos-na

add na fields for pr/er
CanDIG · Sep 23, 2024 · 968f64a · 968f64a
2 parents 23eeb0a + 09d95aa
commit 968f64a
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Showing 6 changed files with 80 additions and 2 deletions.
diff --git a/chord_metadata_service/mohpackets/docs/schema_version.txt b/chord_metadata_service/mohpackets/docs/schema_version.txt
@@ -1 +1 @@
-aff7d68b373affb90ad1bb3a0e50a11371181b9d
+fd2be0bb1831f72571095a6e231e4b74131e070c
diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.json b/chord_metadata_service/mohpackets/docs/schemas/schema.json
@@ -4412,6 +4412,11 @@
                         ],
                         "title": "Er Percent Positive"
                     },
+                    "er_percent_positive_not_available": {
+                        "default": false,
+                        "title": "Er Percent Positive Not Available",
+                        "type": "boolean"
+                    },
                     "pr_status": {
                         "anyOf": [
                             {
@@ -4433,6 +4438,11 @@
                         ],
                         "title": "Pr Percent Positive"
                     },
+                    "pr_percent_positive_not_available": {
+                        "default": false,
+                        "title": "Pr Percent Positive Not Available",
+                        "type": "boolean"
+                    },
                     "her2_ihc_status": {
                         "anyOf": [
                             {
@@ -7342,6 +7352,11 @@
                         ],
                         "title": "Er Percent Positive"
                     },
+                    "er_percent_positive_not_available": {
+                        "default": false,
+                        "title": "Er Percent Positive Not Available",
+                        "type": "boolean"
+                    },
                     "pr_status": {
                         "anyOf": [
                             {
@@ -7363,6 +7378,11 @@
                         ],
                         "title": "Pr Percent Positive"
                     },
+                    "pr_percent_positive_not_available": {
+                        "default": false,
+                        "title": "Pr Percent Positive Not Available",
+                        "type": "boolean"
+                    },
                     "her2_ihc_status": {
                         "anyOf": [
                             {
@@ -9986,6 +10006,11 @@
                         ],
                         "title": "Er Percent Positive"
                     },
+                    "er_percent_positive_not_available": {
+                        "default": false,
+                        "title": "Er Percent Positive Not Available",
+                        "type": "boolean"
+                    },
                     "pr_status": {
                         "anyOf": [
                             {
@@ -10007,6 +10032,11 @@
                         ],
                         "title": "Pr Percent Positive"
                     },
+                    "pr_percent_positive_not_available": {
+                        "default": false,
+                        "title": "Pr Percent Positive Not Available",
+                        "type": "boolean"
+                    },
                     "her2_ihc_status": {
                         "anyOf": [
                             {

diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.md b/chord_metadata_service/mohpackets/docs/schemas/schema.md
@@ -726,8 +726,10 @@ Retrieves a single donor along with all related clinical data, organized in a ne
       "cea_not_available": false,
       "er_status": "Cannot be determined",
       "er_percent_positive": 0,
+      "er_percent_positive_not_available": false,
       "pr_status": "Cannot be determined",
       "pr_percent_positive": 0,
+      "pr_percent_positive_not_available": false,
       "her2_ihc_status": "Cannot be determined",
       "her2_ish_status": "Cannot be determined",
       "hpv_ihc_status": "Cannot be determined",
@@ -1050,8 +1052,10 @@ Used by the query service to return donors along with their sample IDs, treatmen
       "cea_not_available": false,
       "er_status": "Cannot be determined",
       "er_percent_positive": 0,
+      "er_percent_positive_not_available": false,
       "pr_status": "Cannot be determined",
       "pr_percent_positive": 0,
+      "pr_percent_positive_not_available": false,
       "her2_ihc_status": "Cannot be determined",
       "her2_ish_status": "Cannot be determined",
       "hpv_ihc_status": "Cannot be determined",
@@ -2328,8 +2332,10 @@ uBooleanEnum
   "cea_not_available": false,
   "er_status": "Cannot be determined",
   "er_percent_positive": 0,
+  "er_percent_positive_not_available": false,
   "pr_status": "Cannot be determined",
   "pr_percent_positive": 0,
+  "pr_percent_positive_not_available": false,
   "her2_ihc_status": "Cannot be determined",
   "her2_ish_status": "Cannot be determined",
   "hpv_ihc_status": "Cannot be determined",
@@ -2533,6 +2539,7 @@ continued
 
 |Name|Type|Required|Restrictions|Description|
 |---|---|---|---|---|
+|er_percent_positive_not_available|boolean|false|none|none|
 |pr_status|any|false|none|none|
 
 anyOf
@@ -2569,6 +2576,7 @@ continued
 
 |Name|Type|Required|Restrictions|Description|
 |---|---|---|---|---|
+|pr_percent_positive_not_available|boolean|false|none|none|
 |her2_ihc_status|any|false|none|none|
 
 anyOf
@@ -7110,8 +7118,10 @@ TreatmentTypeEnum
       "cea_not_available": false,
       "er_status": "Cannot be determined",
       "er_percent_positive": 0,
+      "er_percent_positive_not_available": false,
       "pr_status": "Cannot be determined",
       "pr_percent_positive": 0,
+      "pr_percent_positive_not_available": false,
       "her2_ihc_status": "Cannot be determined",
       "her2_ish_status": "Cannot be determined",
       "hpv_ihc_status": "Cannot be determined",
@@ -7365,8 +7375,10 @@ continued
   "cea_not_available": false,
   "er_status": "Cannot be determined",
   "er_percent_positive": 0,
+  "er_percent_positive_not_available": false,
   "pr_status": "Cannot be determined",
   "pr_percent_positive": 0,
+  "pr_percent_positive_not_available": false,
   "her2_ihc_status": "Cannot be determined",
   "her2_ish_status": "Cannot be determined",
   "hpv_ihc_status": "Cannot be determined",
@@ -7567,6 +7579,7 @@ continued
 
 |Name|Type|Required|Restrictions|Description|
 |---|---|---|---|---|
+|er_percent_positive_not_available|boolean|false|none|none|
 |pr_status|any|false|none|none|
 
 anyOf
@@ -7603,6 +7616,7 @@ continued
 
 |Name|Type|Required|Restrictions|Description|
 |---|---|---|---|---|
+|pr_percent_positive_not_available|boolean|false|none|none|
 |her2_ihc_status|any|false|none|none|
 
 anyOf
@@ -12063,8 +12077,10 @@ continued
   "cea_not_available": false,
   "er_status": "Cannot be determined",
   "er_percent_positive": 0,
+  "er_percent_positive_not_available": false,
   "pr_status": "Cannot be determined",
   "pr_percent_positive": 0,
+  "pr_percent_positive_not_available": false,
   "her2_ihc_status": "Cannot be determined",
   "her2_ish_status": "Cannot be determined",
   "hpv_ihc_status": "Cannot be determined",
@@ -12267,6 +12283,7 @@ continued
 
 |Name|Type|Required|Restrictions|Description|
 |---|---|---|---|---|
+|er_percent_positive_not_available|boolean|false|none|none|
 |pr_status|any|false|none|none|
 
 anyOf
@@ -12303,6 +12320,7 @@ continued
 
 |Name|Type|Required|Restrictions|Description|
 |---|---|---|---|---|
+|pr_percent_positive_not_available|boolean|false|none|none|
 |her2_ihc_status|any|false|none|none|
 
 anyOf
@@ -12423,8 +12441,10 @@ continued
       "cea_not_available": false,
       "er_status": "Cannot be determined",
       "er_percent_positive": 0,
+      "er_percent_positive_not_available": false,
       "pr_status": "Cannot be determined",
       "pr_percent_positive": 0,
+      "pr_percent_positive_not_available": false,
       "her2_ihc_status": "Cannot be determined",
       "her2_ish_status": "Cannot be determined",
       "hpv_ihc_status": "Cannot be determined",

diff --git a/chord_metadata_service/mohpackets/docs/schemas/schema.yml b/chord_metadata_service/mohpackets/docs/schemas/schema.yml
@@ -132,6 +132,10 @@ components:
           - type: number
           - type: 'null'
           title: Er Percent Positive
+        er_percent_positive_not_available:
+          default: false
+          title: Er Percent Positive Not Available
+          type: boolean
         er_status:
           anyOf:
           - $ref: '#/components/schemas/ErPrHpvStatusEnum'
@@ -164,6 +168,10 @@ components:
           - type: number
           - type: 'null'
           title: Pr Percent Positive
+        pr_percent_positive_not_available:
+          default: false
+          title: Pr Percent Positive Not Available
+          type: boolean
         pr_status:
           anyOf:
           - $ref: '#/components/schemas/ErPrHpvStatusEnum'
@@ -246,6 +254,10 @@ components:
           - type: number
           - type: 'null'
           title: Er Percent Positive
+        er_percent_positive_not_available:
+          default: false
+          title: Er Percent Positive Not Available
+          type: boolean
         er_status:
           anyOf:
           - $ref: '#/components/schemas/ErPrHpvStatusEnum'
@@ -278,6 +290,10 @@ components:
           - type: number
           - type: 'null'
           title: Pr Percent Positive
+        pr_percent_positive_not_available:
+          default: false
+          title: Pr Percent Positive Not Available
+          type: boolean
         pr_status:
           anyOf:
           - $ref: '#/components/schemas/ErPrHpvStatusEnum'
@@ -1360,6 +1376,10 @@ components:
           - type: number
           - type: 'null'
           title: Er Percent Positive
+        er_percent_positive_not_available:
+          default: false
+          title: Er Percent Positive Not Available
+          type: boolean
         er_status:
           anyOf:
           - $ref: '#/components/schemas/ErPrHpvStatusEnum'
@@ -1392,6 +1412,10 @@ components:
           - type: number
           - type: 'null'
           title: Pr Percent Positive
+        pr_percent_positive_not_available:
+          default: false
+          title: Pr Percent Positive Not Available
+          type: boolean
         pr_status:
           anyOf:
           - $ref: '#/components/schemas/ErPrHpvStatusEnum'

diff --git a/chord_metadata_service/mohpackets/migrations/0001_initial.py b/chord_metadata_service/mohpackets/migrations/0001_initial.py
@@ -1,4 +1,4 @@
-# Generated by Django 5.0.6 on 2024-09-15 19:36
+# Generated by Django 5.0.6 on 2024-09-23 21:47
 
 import chord_metadata_service.mohpackets.models
 import django.contrib.postgres.fields
@@ -135,8 +135,10 @@ class Migration(migrations.Migration):
                 ('cea_not_available', models.BooleanField(default=False)),
                 ('er_status', models.CharField(blank=True, max_length=64, null=True)),
                 ('er_percent_positive', models.FloatField(blank=True, null=True)),
+                ('er_percent_positive_not_available', models.BooleanField(default=False)),
                 ('pr_status', models.CharField(blank=True, max_length=64, null=True)),
                 ('pr_percent_positive', models.FloatField(blank=True, null=True)),
+                ('pr_percent_positive_not_available', models.BooleanField(default=False)),
                 ('her2_ihc_status', models.CharField(blank=True, max_length=64, null=True)),
                 ('her2_ish_status', models.CharField(blank=True, max_length=64, null=True)),
                 ('hpv_ihc_status', models.CharField(blank=True, max_length=64, null=True)),

diff --git a/chord_metadata_service/mohpackets/models.py b/chord_metadata_service/mohpackets/models.py
@@ -400,8 +400,10 @@ class Biomarker(models.Model):
     cea_not_available = models.BooleanField(default=False)
     er_status = models.CharField(max_length=64, null=True, blank=True)
     er_percent_positive = models.FloatField(null=True, blank=True)
+    er_percent_positive_not_available = models.BooleanField(default=False)
     pr_status = models.CharField(max_length=64, null=True, blank=True)
     pr_percent_positive = models.FloatField(null=True, blank=True)
+    pr_percent_positive_not_available = models.BooleanField(default=False)
     her2_ihc_status = models.CharField(max_length=64, null=True, blank=True)
     her2_ish_status = models.CharField(max_length=64, null=True, blank=True)
     hpv_ihc_status = models.CharField(max_length=64, null=True, blank=True)
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		aff7d68b373affb90ad1bb3a0e50a11371181b9d
		fd2be0bb1831f72571095a6e231e4b74131e070c